After the war ended he was posted for frontier duty in Texas and the surrounding territories. Participating in the Utah Expedition in 1858 and 1859 Ruggles went on leave of absence for health reasons and stayed absent till the beginning of the American Civil War.[1]

With the outbreak of the Civil War, Ruggles resigned his commission in the U.S. Army on May 7, 1861[2] Appointed a Brigadier General of Militia and Colonel in the Provisional Army of Virginia he was given command of the Aquia District in May 1861.[3] There Ruggles set up shore batteries to block the Chesapeake Bay. After exchanging fire with the Union Navy Ruggles' troops resisted a landing party and prevented a Union beachhead in the Battle of Mathias Point.

On August 9, 1861, he was promoted to Brigadier General and assigned command of a brigade in Gen. Braxton Bragg's Army of Pensacola in Florida. Simultaneously commanding the District of Northern Alabama, Ruggle's brigade moved westwards into Mississippi with Bragg in February 1862. Ruggles now was assigned to command a division in Bragg's Corps in the Army of Mississippi. Under overall command of General Albert Sidney Johnston they marched northwards for the Shiloh Campaign.[3]

During the battle of Shiloh (Union name Pittsburg Landing) on April 6–7, 1862, Gen. Ruggles, on Sunday, April 6, saw repeated Confederate charges against the Union line known as "The Hornets Nest" fail. He sent word to his commanders to "Get every gun you can find." Subsequently, artillery was collected from every part of the field and lined up in a row of 62 cannons, now known as "Ruggles's Battery" (the biggest concentration of Artillery ever seen before), which hammered the Hornets Nest until the last Confederate charge broke the Union line at around 5:30 p.m., forcing it to surrender, 12 hours after the battle had started.

From August 15 to August 29, 1862 Ruggles was in command of the Port Hudson position on the Mississippi in Louisiana and supervised the planning and initial construction of fortifications in that region. On the 29th he was ordered by Breckinridge to move with some of his troops to the state of Mississippi.[5] For the rest of the war he performed mostly administrative duties and was named as the head of the prison system in 1865. He oversaw the final exchange of Union prisoners of war at the end of the conflict.

After the war, Ruggles was a real estate agent and a farmer in Virginia. He later served as a member of the West Point Board of Visitors.[2] He died in Fredericksburg, Virginia in 1897; and rests there on the Confederate Cemetery.